| MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from reference genomes, allowing orders of magnitude speedups and unambiguous taxonomic assignments.
Although MetaPhlAn can use both BlastN and BowTie2 in the read-to-marker mapping step, this Galaxy module uses only BowTie2 for computational reasons. For additional information about MetaPhlAn and the MetaPhlAn command line package, please refer to http://huttenhower.sph.harvard.edu/metaphlan or to the paper reported below. Please notice that most of the additional parameters that can be tuned with the command line version are set here to the default values. Inputs The input file must be a multi-fasta file containing metagenomic reads loaded with the "Get Data" module in the left panel. Reads can be as short as ~40 nt although lengths higher than 70 nt are recommended. A synthetic metagenome you can use as sample input is available at https://bitbucket.org/nsegata/metaphlan/wiki/LC1.fna. Outputs The output is a two column tab-separated plain file reporting the predicted microbial clades present in the metagenomic samples and the corresponding relative abundances. All taxonomic levels from domain to species will be reported and higher taxonomic levelis contain the sum of the abundances of its taxonomic leaf nodes (usually species) and, possibly, some lower level "unclassified" clades. |
hg clone https://toolshed.g2.bx.psu.edu/repos/george-weingart/metaphlan
| Repository package_numpy_1_7 revision 0c288abd2a1e owned by devteam |
| Repository package_bowtie2_2_1_0 revision 017a00c265f1 owned by devteam |
| Name | Version | Type | |
|---|---|---|---|
| bowtie2 | 2.1.0 | package | |
| metaphlan | 1.7.0 | package | |
| numpy | 1.7 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| metagenomic profiler | 1.7.0 | any | |